DeepClustering

Flag: --add-self-aln

Flag: --aln-out

Flag: --anchored-swipe

Flag: --anchor-score

Flag: --anchor-window

Flag: --ants

Flag: --approx-backtrace

Minimum approximate identity % to report an alignment/to cluster sequences.

Flag: --band-bin

Flag: --bcutoff

Number of query bins for seed search.

Flag: --bmatch

Flag: --bmismatch

Flag: --bootstrap-block

Flag: --cbs-angle

Flag: --cbs-err-tolerance

Flag: --cbs-it-limit

Flag: --cbs-matrix-scale

Flag: --cbs-window

Flag: --centroid-factor

Flag: --chaining-len-cap

Flag: --chaining-maxgap

Flag: --chaining-maxnodes

Flag: --chaining-min-nodes

Flag: --chaining-range-cover

Flag: --chaining-stacked-hsp-ratio

Flag: --chunk-size-multiplier

Flag: --classic-band

Clustering algorithm ('mcl')

Filename for dumping the graph or reading the graph if cluster-restart.

Restart clustering from dumped graph.

Clustering similarity measure.

Clustering steps.

Threshold for the similarity measure.

Flag: --col-bin

Composition based statistics mode.

Flag: --cutoff-score-8bit

Path to the target DIAMOND database file.

Effective database size (in letters).

Type of sequences in database file (nucl/prot).

Flag: --deque_bucket_size

Flag: --d_exp

Flag: --diag-filter-cov

Flag: --diag-filter-id

Flag: --diag-min-estimate

Flag: --d_new

Maximum e-value to report alignments.

Chunk size for adaptive ranking.

Extension mode.

Flag: --ext-yield

Flag: --family-cap

Flag: --family-counts

Flag: --fast-tsv

Trace point fetch size.

Flag: --file1

Flag: --file2

File buffer size in bytes.

Flag: --freq-treshold // TYPO: This typo exists in the diamond cli source.

Flag: --full-sw-len

Flag: --gapped-filter-diag-score

Flag: --gapped-filter-evalue1

Flag: --gapped-filter-window

Flag: --graph-algo

Flag: --hamming-ext

Flag: --hard-masked

Flag: --hash_join_swap

Use header lines in tabular output format.

Flag: --idl

Flag: --idn

Flag: --idr

Ignore warnings

Flag: --join-ht-factor

Flag: --join-split-key-len

Flag: --join-split-size

Flag: --key2

Rank sequences based on kmer frequency in linear stage.

Flag: --left-most-interval

Flag: --length-ratio-threshold

Flag: --load-balancing

Enable even more verbose terminal output, which is also written to a file named diamond.log is the current working directory.

Flag: --log-extend

Flag: --log-query

Flag: --log-subject

Flag: --mapany

Masking algorithm.

Flag: --max-cells

Maximum seed frequency.

Flag: --max-indirection

Flag: --max-motif-len

Flag: --max-swipe-dp

MCL chunk size per thread.

MCL expansion coefficient.

MCL inflation coefficient.

MCL maximum iterations.

Do not symmetrize the transition matrix before clustering.

MCL switch to sparse matrix computation.

Some stats about the connected components in MCL.

Minimum coverage percentage of the cluster member sequence.

Flag: --memory-intervals

Memory limit in GB

Flag: --min-band-overlap

Flag: --minimizer-window

Flag: --min-len-ratio

Flag: --min-realign-overhang

Flag: --min_task_trace_pts

Key: --mmseqs-compat

TODO: this flag appears to be unused.

Softmask abundant motifs.

Minimum mutual coverage percentage of the cluster member and representative sequence.

Flag: --narrow-band-cov

Flag: --narrow-band-factor

Flag: --neighborhood-score

TODO: this flag appears to be unused.

Flag: --no_8bit_extension

Disable auto appending of DAA and DMND file extensions.

Key: --no-block-size-limit

Flag: --no_chaining_merge_hsps

Flag: --no-dict

Flag: --no-forward-fp

Flag: --no-logfile

Print raw seqids without parsing

Disable ranking heuristic.

Flag: --no-reextend

Flag: --no-ref-masking

Flag: --no-reorder

Flag: --no-swipe-realign

Do not unlink temporary files.

Flag: --oid-list

Path to the output file. If this parameter is omitted, the results will be written to the standard output and all other program output will be suppressed.

Flag: --output-fp

Flag: --output-hits

Flag: --palign

Flag: --path-cutoff

Flag: --p_best

Flag: --pipeline-short

Flag: --prefix-scan

Flag: --query-count

Flag: --query-match-distance-threshold

Flag: --query-memory

Disable all terminal output.

Flag: --radix-bits

Flag: --radix-cluster-buffered

Flag: --rank-factor

Flag: --ranking-cutoff-bitscore

Flag: --score-drop-factor

Flag: --raw

Flag: --reassign-max

Flag: --reassign-overlap

Flag: --reassign-ratio

Flag: --relaxed-evalue-factor

TODO: this flag appears to be unused.

Flag: --reverse

Flag: --rho

Per-round approx-id cutoffs for cascaded clustering.

Per-round coverage cutoffs for cascaded clustering.

Flag: --score-estimate-factor

Flag: --score-ratio

Flag: --seed-hit-density

Flag: --seed-weight | -w

Flag: --self

Flag: --short-query-max-len

Flag: --short-query-ungapped-bitscore

Flag: --short-seqids

Flag: --simple-freq

Flag: --sketch-size

Soft masking.

Flag: --sort-join

Flag: --space-penalty

Flag: --store-query-quality

Flag: --strict-gvc

Flag: --superblock

Flag: --swipe-chunk-size

Flag: --swipe-task-size

Maximum tandem repeat period to consider (50)

Minimum repeat probability for masking.

Use tantan masking in ungapped mode

Flag: --target-bias

Number of target sequences to fetch for seed extension.

Flag: --target_hard_cap

Flag: --target-parallel-verbosity

Directory for temporary files.

Number of CPU threads.

Flag: --tile-size

Flag: --timeout

Diamond subcommand.

Flag: --trace-pt-fetch-size

Flag: --transcript-len-estimate

Flag: --tree

Flag: --tsv-read-size

TODO: seems to only be used by benchmark?

Flag: --ungapped-evalue

Flag: --ungapped-evalue-short

Flag: --ungapped-window

Flag: --upgma-dist

Flag: --upgma-edge-limit

Flag: --upgma-input

Flag: --use-dataset-field

Flag: --sw

Enable more verbose terminal output.

Flag: --weighted-gvc